Methods for influenza modelization

Description

Function epimem is used to calculate the threshold for influenza epidemic using historical records (surveillance rates).
The method to calculate the threshold is described in the Moving Epidemics Method (MEM) used to monitor influenza activity in a weekly surveillance system.

Usage

epimem(i.data, i.type = 2, i.level = 0.95, i.type.curve = 2, 
       i.level.curve = 0.95, i.type.threshold = 5, 
       i.level.threshold = 0.95, i.n.max = -1, i.tails = 1, 
       i.type.boot = "norm", i.iter.boot = 10000, i.method = 2, 
       i.param = 2.8, i.levels = c(0.40,0.90,0.975), i.seasons = 10)
## S3 method for class 'flu'
print(x, ...)
## S3 method for class 'flu'
summary(object, ...)
## S3 method for class 'flu'
plot(x, ...)

Arguments

Details

Input data is a data frame containing rates that represent historical influenza surveillance data. It can start and end at any given week (tipically at week 40th), and rates can be expressed as per 100,000 inhabitants (or per consultations, if population is not available) or any other scale.
Parameters i.type, i.type.threshold and i.type.curve defines how to calculate confidence intervals along the process.
i.type.curve is used for calculating the typical influenza curve, i.type.threshold is used to calculate the pre and post epidemic threshold and i.type is used for any other confidende interval used in the method.
All three parameters must be a number between 1 and 6:

Option 4 uses two more parameters: i.type.boot indicates which bootstrap method to use. The values are the same of those of the boot.ci function. Parameter i.iter.boot indicates the number of bootstrap samples to use. See boot for more information about this topic.
Parameters i.level, i.level.threshold and i.level.curve indicates, respectively, the level of the confidence intervals described above.
The i.n.max parameter indicates how many pre epidemic values to use to calculate the threshold. A value of -1 indicates the program to use an appropiate number of points depending on the number of seasons provided as input. i.tails tells the program to use 1 or 2 tailed confidence intervals when calculating the threshold (1 is recommended).
Parameters i.method and i.param indicates how to find the optimal timing of the epidemics. See epitiming for details on the values this parameters can have.

Value

epimem returns an object of class flu. An object of class flu is a list containing at least the following components:

Author(s)

Jose E. Lozano Alonso <lozalojo@jcyl.es>.

References

Vega T., Lozano J.E. (2004) Modelling influenza epidemic - can we detect the beginning and predict the intensity and duration? International Congress Series 1263 (2004) 281-283.
Vega T., Lozano J.E. (2012) Influenza surveillance in Europe: establishing epidemic thresholds by the Moving Epidemic Method. Influenza and Other Respiratory Viruses, DOI:10.1111/j.1750-2659.2012.00422.x.

Examples

## Castilla y Leon Influenza Rates data 
data(flucyl)
## Finds the timing of the first season: 2001/2002
epi<-epimem(flucyl)
print(epi)
summary(epi)
plot(epi)

Results